Findings published on Friday reveal a sharp improvement since August 2017, when GPonline reported that more than four out of five online services were considered unsafe by the regulator.
But the quality of online GP services remains far below the standard set by NHS GP practices - of which 89% are rated good or outstanding on safety by the CQC, with just 2% inadequate on this measure.
Findings from a CQC report published on 23 March are based on inspections of 40 online-only providers currently registered with the CQC. The regulator does not currently publish full ratings for these services as it does for NHS providers - but expects to begin doing so from April 2018.
Safety concerns identified by the CQC with online providers included problems with inappropriate prescribing of antibiotics, opioid-based medicines and asthma medication; problems with child safeguarding; and failing to collect patient data or feed it back to patients' NHS GP, the report said.
Safety is one of five key areas that the regulator's assessments of health and care services focus on. The other four cover whether services are caring, effective, well-led and responsive to patients' needs.
Despite problems with safety, as of 28 February the CQC found that 97% of online services were caring, and 90% were meeting requirements around being responsive.
RCGP chair Professor Helen Stokes-Lampard said: 'It’s absolutely right that the CQC holds organisations that provide online primary care services to the same high standards as any other healthcare provider, to ensure that they are delivering safe, high-quality, and compassionate care for patients - and it’s reassuring to see that a greater proportion are providing safe care than last year.
'But it’s very concerning to see that even now, 43% of online consultation providers have been deemed unsafe in some respect. When our patients’ health is at risk urgent, swift action must be taken to comprehensively address these before the service is rolled out further.
'The college is currently developing guidance for patients, GPs and commissioners who are considering alternatives to face-to-face consultations, to encourage them to only do so after careful consideration of all potential risks and benefits.'
CQC chief inspector of general practice Professor Steve Field said: 'New methods of service delivery that increase access to care and give patients more control over how and when they see a GP have huge potential not only for patients but for the wider health system.
'However, while innovation should be encouraged, it must never come at the expense of quality. As with all healthcare services, patient safety must be at the heart of all decisions around what kind of care is offered and how it is delivered.'
The safety warning over online GP services comes as the GP at Hand service - which offers online video consultations to NHS patients - continues to grow rapidly.
GP at Hand has been rated 'good' overall by the CQC. However, an inspection report on Babylon - the private online provider whose technology is behind the GP at Hand service - is among those that fed into the report on online GP services.
The report on Babylon - published last December after a High Court bid by the company to prevent its release failed - found that 'in some areas, this service was not providing safe care in accordance with the relevant regulations'.
Babylon has strongly criticised the CQC report on its services, and said 'narrow concerns' highlighted by the regulator 'do not apply to the GP at Hand service'. A Babylon spokesman said: 'Babylon welcomes the CQC publicly restating its commitment to learning alongside providers who offer new care models or use new technology to encourage innovation.'
The company highlighted comments from the CQC that its report on Babylon placed it in 'the top quartile of most favourable reports carried out by the CQC' and that its 'services were safe, effective, caring, responsive and well-led'.